Starting phenix.real_space_refine on Thu Dec 7 23:48:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwc_20505/12_2023/6pwc_20505.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwc_20505/12_2023/6pwc_20505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwc_20505/12_2023/6pwc_20505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwc_20505/12_2023/6pwc_20505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwc_20505/12_2023/6pwc_20505.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwc_20505/12_2023/6pwc_20505.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 3562 2.51 5 N 1065 2.21 5 O 1227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5879 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 1824 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'PTRANS': 10, 'TRANS': 312} Chain breaks: 2 Unresolved non-hydrogen bonds: 779 Unresolved non-hydrogen angles: 1003 Unresolved non-hydrogen dihedrals: 677 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 9, 'TYR:plan': 14, 'ASN:plan1': 13, 'TRP:plan': 4, 'ASP:plan': 8, 'PHE:plan': 17, 'GLU:plan': 6, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 475 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 27 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 1935 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 324} Unresolved non-hydrogen bonds: 863 Unresolved non-hydrogen angles: 1078 Unresolved non-hydrogen dihedrals: 721 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 21, 'TYR:plan': 11, 'ASN:plan1': 14, 'HIS:plan': 8, 'PHE:plan': 12, 'GLU:plan': 24, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 522 Chain: "H" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1072 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 184} Chain breaks: 3 Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 7, 'TRP:plan': 5, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 307 Chain: "L" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1021 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 172} Chain breaks: 2 Unresolved non-hydrogen bonds: 411 Unresolved non-hydrogen angles: 522 Unresolved non-hydrogen dihedrals: 360 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 1, 'TYR:plan': 10, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 7, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 278 Time building chain proxies: 4.12, per 1000 atoms: 0.70 Number of scatterers: 5879 At special positions: 0 Unit cell: (161.867, 106.193, 90.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1227 8.00 N 1065 7.00 C 3562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS H 59 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.5 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 17 sheets defined 30.4% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'R' and resid 59 through 91 Processing helix chain 'R' and resid 92 through 94 No H-bonds generated for 'chain 'R' and resid 92 through 94' Processing helix chain 'R' and resid 98 through 129 Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 137 through 172 Processing helix chain 'R' and resid 172 through 179 removed outlier: 3.959A pdb=" N LYS R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 200 Processing helix chain 'R' and resid 201 through 205 Processing helix chain 'R' and resid 218 through 220 No H-bonds generated for 'chain 'R' and resid 218 through 220' Processing helix chain 'R' and resid 229 through 245 Processing helix chain 'R' and resid 245 through 269 removed outlier: 3.694A pdb=" N VAL R 267 " --> pdb=" O LEU R 263 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG R 268 " --> pdb=" O THR R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 329 removed outlier: 3.848A pdb=" N VAL R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 4.197A pdb=" N ARG R 323 " --> pdb=" O TYR R 319 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE R 329 " --> pdb=" O MET R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 368 removed outlier: 4.160A pdb=" N ASN R 360 " --> pdb=" O SER R 356 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 368 through 383 Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.775A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 185 through 190 removed outlier: 4.252A pdb=" N LYS L 189 " --> pdb=" O ALA L 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 208 through 211 Processing sheet with id=AA2, first strand: chain 'R' and resid 411 through 413 removed outlier: 3.629A pdb=" N ASN R 411 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR R 413 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 29 removed outlier: 5.898A pdb=" N PHE A 27 " --> pdb=" O VAL A 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 77 removed outlier: 4.036A pdb=" N PHE A 75 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL A 53 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 77 removed outlier: 4.036A pdb=" N PHE A 75 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA7, first strand: chain 'A' and resid 183 through 188 Processing sheet with id=AA8, first strand: chain 'A' and resid 207 through 209 removed outlier: 6.065A pdb=" N TYR A 208 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N SER A 330 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL A 228 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA A 239 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS A 250 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AB1, first strand: chain 'H' and resid 13 through 15 removed outlier: 5.888A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 13 through 15 Processing sheet with id=AB3, first strand: chain 'H' and resid 130 through 133 removed outlier: 5.927A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER H 187 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL H 179 " --> pdb=" O SER H 187 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 161 through 164 Processing sheet with id=AB5, first strand: chain 'H' and resid 173 through 175 Processing sheet with id=AB6, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB7, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.236A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 115 through 119 removed outlier: 6.105A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR L 179 " --> pdb=" O GLN L 161 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN L 159 " --> pdb=" O THR L 181 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2088 1.34 - 1.46: 1158 1.46 - 1.58: 2664 1.58 - 1.70: 0 1.70 - 1.82: 25 Bond restraints: 5935 Sorted by residual: bond pdb=" C LYS A 355 " pdb=" N PRO A 356 " ideal model delta sigma weight residual 1.341 1.376 -0.035 1.60e-02 3.91e+03 4.87e+00 bond pdb=" C MET R 120 " pdb=" N PRO R 121 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.20e-02 6.94e+03 3.52e+00 bond pdb=" C VAL R 201 " pdb=" N PRO R 202 " ideal model delta sigma weight residual 1.335 1.356 -0.022 1.19e-02 7.06e+03 3.35e+00 bond pdb=" C LEU R 317 " pdb=" N PRO R 318 " ideal model delta sigma weight residual 1.336 1.357 -0.022 1.25e-02 6.40e+03 2.98e+00 bond pdb=" CA VAL R 201 " pdb=" C VAL R 201 " ideal model delta sigma weight residual 1.523 1.537 -0.014 9.20e-03 1.18e+04 2.31e+00 ... (remaining 5930 not shown) Histogram of bond angle deviations from ideal: 102.44 - 108.73: 419 108.73 - 115.02: 3548 115.02 - 121.31: 2325 121.31 - 127.59: 1948 127.59 - 133.88: 40 Bond angle restraints: 8280 Sorted by residual: angle pdb=" C ALA R 200 " pdb=" N VAL R 201 " pdb=" CA VAL R 201 " ideal model delta sigma weight residual 120.33 125.09 -4.76 8.00e-01 1.56e+00 3.54e+01 angle pdb=" CA VAL R 201 " pdb=" C VAL R 201 " pdb=" N PRO R 202 " ideal model delta sigma weight residual 120.83 122.82 -1.99 6.10e-01 2.69e+00 1.07e+01 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 127.59 -6.05 1.91e+00 2.74e-01 1.00e+01 angle pdb=" CA LYS A 95 " pdb=" C LYS A 95 " pdb=" N PRO A 96 " ideal model delta sigma weight residual 118.44 123.01 -4.57 1.59e+00 3.96e-01 8.25e+00 angle pdb=" CA GLY A 316 " pdb=" C GLY A 316 " pdb=" N ILE A 317 " ideal model delta sigma weight residual 114.62 118.23 -3.61 1.26e+00 6.30e-01 8.20e+00 ... (remaining 8275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.22: 3517 12.22 - 24.43: 24 24.43 - 36.65: 2 36.65 - 48.87: 3 48.87 - 61.08: 2 Dihedral angle restraints: 3548 sinusoidal: 501 harmonic: 3047 Sorted by residual: dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual 93.00 154.08 -61.08 1 1.00e+01 1.00e-02 4.96e+01 dihedral pdb=" CB CYS A 279 " pdb=" SG CYS A 279 " pdb=" SG CYS H 59 " pdb=" CB CYS H 59 " ideal model delta sinusoidal sigma weight residual -86.00 -32.21 -53.79 1 1.00e+01 1.00e-02 3.93e+01 dihedral pdb=" CA TRP H 113 " pdb=" C TRP H 113 " pdb=" N GLY H 114 " pdb=" CA GLY H 114 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 3545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 765 0.036 - 0.072: 268 0.072 - 0.109: 88 0.109 - 0.145: 48 0.145 - 0.181: 3 Chirality restraints: 1172 Sorted by residual: chirality pdb=" CA THR R 115 " pdb=" N THR R 115 " pdb=" C THR R 115 " pdb=" CB THR R 115 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" CA MET R 120 " pdb=" N MET R 120 " pdb=" C MET R 120 " pdb=" CB MET R 120 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CA LEU R 317 " pdb=" N LEU R 317 " pdb=" C LEU R 317 " pdb=" CB LEU R 317 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 1169 not shown) Planarity restraints: 1111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 225 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO R 226 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO R 226 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 226 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 267 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C VAL R 267 " -0.030 2.00e-02 2.50e+03 pdb=" O VAL R 267 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG R 268 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 144 " 0.018 2.00e-02 2.50e+03 1.23e-02 3.03e+00 pdb=" CG TYR R 144 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR R 144 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR R 144 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR R 144 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR R 144 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR R 144 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 144 " -0.001 2.00e-02 2.50e+03 ... (remaining 1108 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 1987 2.86 - 3.37: 5096 3.37 - 3.88: 8881 3.88 - 4.39: 7784 4.39 - 4.90: 15405 Nonbonded interactions: 39153 Sorted by model distance: nonbonded pdb=" O ASN R 240 " pdb=" OG SER R 244 " model vdw 2.345 2.440 nonbonded pdb=" O TYR R 354 " pdb=" OG1 THR R 358 " model vdw 2.376 2.440 nonbonded pdb=" O HIS H 210 " pdb=" N ASN H 214 " model vdw 2.380 2.520 nonbonded pdb=" O ALA A 301 " pdb=" OH TYR A 321 " model vdw 2.393 2.440 nonbonded pdb=" O ALA A 263 " pdb=" OG SER A 266 " model vdw 2.401 2.440 ... (remaining 39148 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.780 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 20.320 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5935 Z= 0.223 Angle : 0.667 7.838 8280 Z= 0.392 Chirality : 0.046 0.181 1172 Planarity : 0.006 0.046 1111 Dihedral : 4.676 21.029 1536 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.24), residues: 1031 helix: 0.54 (0.27), residues: 265 sheet: 0.29 (0.28), residues: 327 loop : -0.60 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP R 193 HIS 0.007 0.004 HIS R 102 PHE 0.002 0.000 PHE R 74 TYR 0.029 0.002 TYR R 344 ARG 0.000 0.000 ARG R 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.671 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0674 time to fit residues: 4.4276 Evaluate side-chains 19 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.703 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 50.0000 chunk 78 optimal weight: 40.0000 chunk 43 optimal weight: 9.9990 chunk 26 optimal weight: 30.0000 chunk 53 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 50.0000 chunk 49 optimal weight: 50.0000 chunk 60 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 5935 Z= 0.267 Angle : 0.604 6.331 8280 Z= 0.348 Chirality : 0.041 0.169 1172 Planarity : 0.005 0.063 1111 Dihedral : 4.740 19.834 1048 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1031 helix: 2.17 (0.30), residues: 269 sheet: -0.19 (0.26), residues: 373 loop : 0.19 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 193 HIS 0.005 0.002 HIS R 300 PHE 0.013 0.001 PHE A 80 TYR 0.015 0.001 TYR R 144 ARG 0.001 0.001 ARG R 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.703 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0598 time to fit residues: 3.4194 Evaluate side-chains 19 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.707 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 50.0000 chunk 26 optimal weight: 30.0000 chunk 94 optimal weight: 7.9990 chunk 102 optimal weight: 30.0000 chunk 84 optimal weight: 50.0000 chunk 93 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5935 Z= 0.238 Angle : 0.594 7.748 8280 Z= 0.339 Chirality : 0.042 0.163 1172 Planarity : 0.005 0.060 1111 Dihedral : 5.117 18.593 1048 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1031 helix: 2.41 (0.30), residues: 276 sheet: -0.59 (0.27), residues: 336 loop : -0.19 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 193 HIS 0.008 0.003 HIS R 300 PHE 0.011 0.001 PHE A 80 TYR 0.014 0.001 TYR R 144 ARG 0.006 0.003 ARG R 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.708 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0607 time to fit residues: 2.9014 Evaluate side-chains 14 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.669 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 30.0000 chunk 71 optimal weight: 8.9990 chunk 49 optimal weight: 0.0030 chunk 10 optimal weight: 5.9990 chunk 45 optimal weight: 50.0000 chunk 63 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 40.0000 chunk 89 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 83 optimal weight: 30.0000 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.6178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5935 Z= 0.163 Angle : 0.492 7.389 8280 Z= 0.269 Chirality : 0.040 0.148 1172 Planarity : 0.004 0.052 1111 Dihedral : 4.380 16.641 1048 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.27), residues: 1031 helix: 2.90 (0.30), residues: 280 sheet: -0.71 (0.28), residues: 317 loop : 0.06 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP R 193 HIS 0.005 0.002 HIS R 300 PHE 0.006 0.001 PHE A 80 TYR 0.014 0.001 TYR R 144 ARG 0.002 0.001 ARG R 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.674 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0597 time to fit residues: 2.8332 Evaluate side-chains 14 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.675 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 51 optimal weight: 50.0000 chunk 90 optimal weight: 0.4980 chunk 25 optimal weight: 20.0000 chunk 33 optimal weight: 30.0000 overall best weight: 7.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.7569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5935 Z= 0.268 Angle : 0.587 6.907 8280 Z= 0.332 Chirality : 0.041 0.149 1172 Planarity : 0.005 0.045 1111 Dihedral : 5.192 21.570 1048 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1031 helix: 2.69 (0.30), residues: 277 sheet: -1.08 (0.27), residues: 330 loop : -0.42 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 193 HIS 0.006 0.002 HIS R 300 PHE 0.010 0.001 PHE A 9 TYR 0.016 0.001 TYR R 144 ARG 0.002 0.001 ARG R 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.619 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0566 time to fit residues: 2.5567 Evaluate side-chains 14 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.609 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 20.0000 chunk 52 optimal weight: 0.3980 chunk 97 optimal weight: 50.0000 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.7480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5935 Z= 0.134 Angle : 0.471 7.382 8280 Z= 0.253 Chirality : 0.040 0.144 1172 Planarity : 0.004 0.043 1111 Dihedral : 4.305 17.296 1048 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.27), residues: 1031 helix: 3.11 (0.30), residues: 280 sheet: -0.95 (0.28), residues: 317 loop : -0.27 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP R 193 HIS 0.004 0.002 HIS R 300 PHE 0.009 0.001 PHE A 9 TYR 0.014 0.001 TYR R 144 ARG 0.000 0.000 ARG R 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.684 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0625 time to fit residues: 3.0041 Evaluate side-chains 14 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.698 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 56 optimal weight: 40.0000 chunk 84 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 61 optimal weight: 30.0000 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 59 optimal weight: 9.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.8003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5935 Z= 0.170 Angle : 0.492 7.269 8280 Z= 0.267 Chirality : 0.039 0.146 1172 Planarity : 0.004 0.041 1111 Dihedral : 4.308 19.773 1048 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.27), residues: 1031 helix: 3.29 (0.30), residues: 281 sheet: -1.02 (0.28), residues: 319 loop : -0.36 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP R 193 HIS 0.005 0.002 HIS R 300 PHE 0.009 0.001 PHE A 9 TYR 0.013 0.001 TYR R 144 ARG 0.001 0.000 ARG R 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.715 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0615 time to fit residues: 2.8470 Evaluate side-chains 14 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.721 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 50.0000 chunk 63 optimal weight: 6.9990 chunk 68 optimal weight: 50.0000 chunk 49 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 96 optimal weight: 50.0000 chunk 87 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.9274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5935 Z= 0.252 Angle : 0.597 7.320 8280 Z= 0.337 Chirality : 0.041 0.150 1172 Planarity : 0.005 0.048 1111 Dihedral : 5.488 24.732 1048 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1031 helix: 2.95 (0.29), residues: 272 sheet: -1.54 (0.28), residues: 308 loop : -0.91 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 193 HIS 0.006 0.002 HIS R 300 PHE 0.014 0.001 PHE A 9 TYR 0.017 0.001 TYR R 144 ARG 0.002 0.001 ARG R 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.713 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0602 time to fit residues: 2.7484 Evaluate side-chains 14 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 40.0000 chunk 56 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 30.0000 chunk 28 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 88 optimal weight: 40.0000 chunk 93 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.9542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5935 Z= 0.202 Angle : 0.526 7.859 8280 Z= 0.291 Chirality : 0.040 0.143 1172 Planarity : 0.004 0.044 1111 Dihedral : 4.907 21.722 1048 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.27), residues: 1031 helix: 2.93 (0.30), residues: 280 sheet: -1.40 (0.29), residues: 304 loop : -0.94 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 193 HIS 0.005 0.002 HIS R 300 PHE 0.009 0.001 PHE A 9 TYR 0.015 0.001 TYR R 144 ARG 0.001 0.001 ARG R 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.596 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0581 time to fit residues: 2.5509 Evaluate side-chains 14 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.701 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 8.9990 chunk 68 optimal weight: 50.0000 chunk 103 optimal weight: 30.0000 chunk 95 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 8 optimal weight: 0.0060 chunk 63 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 65 optimal weight: 50.0000 chunk 87 optimal weight: 50.0000 chunk 25 optimal weight: 0.9980 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.9710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5935 Z= 0.166 Angle : 0.488 7.939 8280 Z= 0.265 Chirality : 0.040 0.143 1172 Planarity : 0.004 0.046 1111 Dihedral : 4.541 21.472 1048 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.27), residues: 1031 helix: 3.07 (0.30), residues: 286 sheet: -1.38 (0.29), residues: 310 loop : -0.86 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP R 193 HIS 0.005 0.002 HIS R 300 PHE 0.009 0.001 PHE A 9 TYR 0.013 0.001 TYR R 144 ARG 0.001 0.000 ARG R 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.684 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0592 time to fit residues: 2.7599 Evaluate side-chains 14 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.680 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 50.0000 chunk 82 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 50.0000 chunk 72 optimal weight: 9.9990 chunk 4 optimal weight: 40.0000 chunk 59 optimal weight: 5.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.032980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.022671 restraints weight = 114578.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.022736 restraints weight = 111251.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.022736 restraints weight = 108186.996| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5944 moved from start: 1.0269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5935 Z= 0.258 Angle : 0.581 8.070 8280 Z= 0.326 Chirality : 0.040 0.143 1172 Planarity : 0.005 0.046 1111 Dihedral : 5.239 24.673 1048 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.26), residues: 1031 helix: 2.88 (0.30), residues: 279 sheet: -1.60 (0.30), residues: 287 loop : -1.30 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 193 HIS 0.006 0.002 HIS R 300 PHE 0.012 0.001 PHE A 9 TYR 0.015 0.001 TYR R 144 ARG 0.001 0.001 ARG R 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1117.66 seconds wall clock time: 20 minutes 59.24 seconds (1259.24 seconds total)